6AGZ

Crystal structure of Old Yellow Enzyme from Pichia sp. AKU4542


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 

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Literature

Structural basis of different substrate preferences of two old yellow enzymes from yeasts in the asymmetric reduction of enone compounds.

Horita, S.Kataoka, M.Kitamura, N.Miyakawa, T.Ohtsuka, J.Maejima, Y.Shimomura, K.Nagata, K.Shimizu, S.Tanokura, M.

(2019) Biosci Biotechnol Biochem 83: 456-462

  • DOI: https://doi.org/10.1080/09168451.2018.1543014
  • Primary Citation of Related Structures:  
    6AGZ

  • PubMed Abstract: 

    Old yellow enzymes (OYEs) are potential targets of protein engineering for useful biocatalysts because of their excellent asymmetric reductions of enone compounds. Two OYEs from different yeast strains, Candida macedoniensis AKU4588 OYE (CmOYE) and Pichia sp. AKU4542 OYE (PsOYE), have a sequence identity of 46%, but show different substrate preferences; PsOYE shows 3.4-fold and 39-fold higher catalytic activities than CmOYE toward ketoisophorone and (4S)-phorenol, respectively. To gain insights into structural basis of their different substrate preferences, we have solved a crystal structure of PsOYE, and compared its catalytic site structure with that of CmOYE, revealing the catalytic pocket of PsOYE is wider than that of CmOYE due to different positions of Phe 246 (PsOYE)/Phe 250 (CmOYE) in static Loop 5. This study shows a significance of 3D structural information to explain the different substrate preferences of yeast OYEs which cannot be understood from their amino acid sequences. Abbreviations: OYE: Old yellow enzymes, CmOYE: Candida macedoniensis AKU4588 OYE, PsOYE: Pichia sp. AKU4542 OYE.


  • Organizational Affiliation

    a Department of Applied Biologic al Chemistry , Graduate School of Agricultural and Life Sciences, University of Tokyo , Tokyo , Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Old Yellow Enzyme
A, B
405PichiaMutation(s): 0 
UniProt
Find proteins for A0A5H1ZR30 (Pichia)
Explore A0A5H1ZR30 
Go to UniProtKB:  A0A5H1ZR30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5H1ZR30
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.45α = 90
b = 108.71β = 91.51
c = 89.93γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references